The best possible solution would be the addition of the interlaced (row-interleaved) format that allows to work in window mode (along with the menus if they are shifted just a little bit for L and R) for a long time (without flicker, headache and switching 3D off and on like in active TVs), so an interlaced format would be more than welcome.

Meanwhile, until such a feature is implemented, is it possible to split the viewport in two, assign to each part a synced camera parallel to each other at an interocular distance, and control them simultaneously like you do normally in viewport in order to feed the 3D monitor/TV with a TAB (Top And Bottom) or SBS (Side By Side) signal in fullscreen mode?
EDIT: It would also require to have a custom aspect ratio of 8:9 on each viewport (50% compressed horizontally).

Even that, i.e working in “expert” mode in fullscreen stereo viewport without the menus, would be very helpful.